The result of the Human Genome Project -- the complete sequence of human DNA -- presented several surprises, some of which seemed almost contradictory to long-held beliefs about how our genes work.

The total number of genes, estimated to be about 150,000 only a year before the sequence was completed, is actually only around 30,000, which may at first seem surprisingly small considering the complexity and sophistication of human beings. After all, our genes not only contain the blueprints for building every tissue in the human body, they also describe how to run and maintain the whole organism, control its development, and stably operate the activities of the brain -- all with a margin that allows for evolutionary experiments.

Interestingly, the sequence of the mouse genome, reported in December of 2002, showed an astonishing similarity to ours: 99 percent of the nearly 30,000 genes in a mouse have direct counterparts in man. Yet, we can easily point at several obvious differences between these species: we walk on two legs, mice on four; we can live for 100 years, mice rarely longer than a couple; we talk and play the piano, mice squeak and lack dexterity; and, perhaps most importantly, we think we're a lot smarter than mice.

99 percent of the nearly 30,000 genes in a mouse have direct counterparts in man.

Since the sets of genes in mice and men don't differ that much, the unique features of each organism must depend greatly on how our genes are used. The genes in a mouse follow a different program than the genes in a person. Scientists have recently started to realize the complexity of gene regulation -- how genes become active or inactive at different times during development and later in life. We have long known that proteins bind to DNA and recruit the transcription machinery that initiates expression of a certain gene or, alternately, that proteins may block a gene from transcription. In addition to that, a number of previously unknown ways to control gene expression have emerged in the last few years, some of which depend on parts of the genome that don't encode proteins.

Our genes occupy only about two percent of the human genome. The role of the rest, the so-called "junk" DNA, was long a matter of speculation. The completed sequence has allowed scientists to pull back and consider these huge expanses of DNA "nonsense" from a distance, one chromosome at a time. In the last few years, scientists have noted important functions for these non-coding sequences.